{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS8533DISB/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS8533DISB",
"aliases": [
"jesse-engreitz:THP1-PPIF_promoter_lentiMPRA_BioRep3_RNA_BarcodeSequencing"
],
"assay_term": {
"@id": "/assay-terms/OBI_0002675/",
"assay_slims": [
"reporter"
],
"status": "released",
"term_name": "massively parallel reporter assay"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS8533DISB](/measurement-sets/IGVFDS8533DISB/) has sequence file(s) [IGVFFI4853ZPEU](/sequence-files/IGVFFI4853ZPEU/), [IGVFFI2398KYLW](/sequence-files/IGVFFI2398KYLW/), [IGVFFI7531OBRW](/sequence-files/IGVFFI7531OBRW/) which lack specification of a `sequencing_kit`. Sequence files in a file set associated wtih bulk data should specify a sequencing kit.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_inconsistent_sequencing_kit",
"path": "/measurement-sets/IGVFDS8533DISB/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS8533DISB](/measurement-sets/IGVFDS8533DISB/) has sequence file(s): [IGVFFI4853ZPEU](/sequence-files/IGVFFI4853ZPEU/), [IGVFFI2398KYLW](/sequence-files/IGVFFI2398KYLW/), [IGVFFI7531OBRW](/sequence-files/IGVFFI7531OBRW/) which do not have any `seqspecs`. Sequence files in a file set associated with bulk data are expected to link to a sequence specification file.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_missing_seqspec",
"path": "/measurement-sets/IGVFDS8533DISB/"
},
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS3584HARV](/auxiliary-sets/IGVFDS3584HARV/) has sequence file(s) [IGVFFI4404HHXN](/sequence-files/IGVFFI4404HHXN/), [IGVFFI4975PFEA](/sequence-files/IGVFFI4975PFEA/), [IGVFFI7462HWBH](/sequence-files/IGVFFI7462HWBH/) which lack specification of a `sequencing_kit`. Sequence files in a file set associated wtih bulk data should specify a sequencing kit.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_inconsistent_sequencing_kit",
"path": "/auxiliary-sets/IGVFDS3584HARV/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS3584HARV](/auxiliary-sets/IGVFDS3584HARV/) has sequence file(s): [IGVFFI4404HHXN](/sequence-files/IGVFFI4404HHXN/), [IGVFFI4975PFEA](/sequence-files/IGVFFI4975PFEA/), [IGVFFI7462HWBH](/sequence-files/IGVFFI7462HWBH/) which do not have any `seqspecs`. Sequence files in a file set associated with bulk data are expected to link to a sequence specification file.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_missing_seqspec",
"path": "/auxiliary-sets/IGVFDS3584HARV/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing read names",
"detail": "MPRA Measurement set [IGVFDS8533DISB](/measurement-sets/IGVFDS8533DISB/) links to sequence files: [IGVFFI4853ZPEU](/sequence-files/IGVFFI4853ZPEU/),[IGVFFI2398KYLW](/sequence-files/IGVFFI2398KYLW/),[IGVFFI7531OBRW](/sequence-files/IGVFFI7531OBRW/) that do not specify `read_names`. MPRA measurement set and auxiliary set sequence files are expected to specify a read name.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_MPRA_read_names",
"path": "/measurement-sets/IGVFDS8533DISB/"
},
{
"category": "missing read names",
"detail": "MPRA Auxiliary set [IGVFDS3584HARV](/auxiliary-sets/IGVFDS3584HARV/) links to sequence files: [IGVFFI4404HHXN](/sequence-files/IGVFFI4404HHXN/),[IGVFFI4975PFEA](/sequence-files/IGVFFI4975PFEA/),[IGVFFI7462HWBH](/sequence-files/IGVFFI7462HWBH/) that do not specify `read_names`. MPRA measurement set and auxiliary set sequence files are expected to specify a read name.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_MPRA_read_names",
"path": "/auxiliary-sets/IGVFDS3584HARV/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS3584HARV/",
"accession": "IGVFDS3584HARV",
"aliases": [
"jesse-engreitz:THP1-PPIF_promoter_lentiMPRA_BioRep3_DNA_BarcodeSequencing"
],
"file_set_type": "quantification DNA barcode sequencing",
"status": "preview"
}
],
"award": {
"@id": "/awards/HG011972/",
"component": "functional characterization",
"contact_pi": {
"@id": "/users/6c75dbfa-635e-4a7a-8ec8-9e51e9c380a4/",
"title": "Jesse Engreitz"
},
"title": "Stanford Center for Connecting DNA Variants to Function and Phenotype"
},
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS3011TBLW/",
"accession": "IGVFDS3011TBLW",
"file_set_type": "reporter library",
"status": "preview",
"summary": "reporter library targeting sequence variants in a genomic locus"
}
],
"control_for": [],
"creation_timestamp": "2024-11-23T01:01:11.632353+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO7359LVPI/",
"accession": "IGVFDO7359LVPI",
"aliases": [
"igvf:donor_of_THP1"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI4853ZPEU/",
"accession": "IGVFFI4853ZPEU",
"aliases": [
"jesse-engreitz:THP1-PPIF_promoter_lentiMPRA_BioRep3_RNA_BarcodeSequencing_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-23T01:11:01.823493+00:00",
"file_format": "fastq",
"file_size": 242487131,
"href": "/sequence-files/IGVFFI4853ZPEU/@@download/IGVFFI4853ZPEU.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/23/9a044b5a-05d4-47e8-9ea4-ec9f685717e2/IGVFFI4853ZPEU.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "preview",
"submitted_file_name": "PPIF3_R3_RNA_S9_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2398KYLW/",
"accession": "IGVFFI2398KYLW",
"aliases": [
"jesse-engreitz:THP1-PPIF_promoter_lentiMPRA_BioRep3_RNA_BarcodeSequencing_R3"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-23T01:11:40.421136+00:00",
"file_format": "fastq",
"file_size": 225107180,
"href": "/sequence-files/IGVFFI2398KYLW/@@download/IGVFFI2398KYLW.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/23/022ee26b-d455-4b4e-9e5c-1ba3b2589656/IGVFFI2398KYLW.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "preview",
"submitted_file_name": "PPIF3_R3_RNA_S9_R3_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7531OBRW/",
"accession": "IGVFFI7531OBRW",
"aliases": [
"jesse-engreitz:THP1-PPIF_promoter_lentiMPRA_BioRep3_RNA_BarcodeSequencing_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-23T01:10:27.622268+00:00",
"file_format": "fastq",
"file_size": 225936737,
"href": "/sequence-files/IGVFFI7531OBRW/@@download/IGVFFI7531OBRW.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/23/73a7f187-6089-435d-b2b5-1a4e3a64cfc3/IGVFFI7531OBRW.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "preview",
"submitted_file_name": "PPIF3_R3_RNA_S9_R1_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS1376WOXJ/"
],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"preferred_assay_title": "lentiMPRA",
"protocols": [
"https://www.protocols.io/view/massive-parallel-reporter-assay-mpra-kxygxpmkwl8j/v1"
],
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM5454DSMW/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM5454DSMW",
"aliases": [
"jesse-engreitz:THP1-PPIF_promoter_lentiMPRA_BioRep3"
],
"classifications": [
"cell line"
],
"institutional_certificates": [],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0001253/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:THP-1"
],
"status": "released",
"summary": "THP-1",
"term_name": "THP-1"
}
],
"status": "preview",
"summary": "Homo sapiens (male) THP-1 cell line transduced (lentivirus) with a reporter library",
"taxa": "Homo sapiens"
}
],
"schema_version": "26",
"status": "preview",
"submitted_by": {
"@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
"title": "Michael Montgomery"
},
"submitted_files_timestamp": "2024-11-23T01:08:51.946696+00:00",
"summary": "lentiMPRA integrating a reporter library targeting sequence variants in a genomic locus",
"uuid": "255579a9-491f-469f-b462-36656427601b"
}